Why does the 1 tablespoon of coffee grounds not equal 15 ml

Amongst other things, fats help moderate/impede gluten development, by not allowing water to activate the proteins.

Too much yeast and your dough will be flabby and over-risen.

I've always been taught that baking is a science when it is compared to cooking. Cooking is very much 'to taste' and very individual. There are not as many things that can go wrong with a standard recipe in cooking, and you have a lot more room for creativity. You don't have to look at baking as that precise. However, unlike cooking, where you can add or subtract from a recipe with no real harm to physical structure, that does not hold in baking. For examlple, if you feel that there is too much salt in a recipe, cutting back can (and most likely will) have a cascading effect through the ingredient chain. You have to understand your ingredients and the effect they have on other ingredients. That is what makes baking a more precise science.
And in terms of flour, it is often the most 'ranged' ingredient. Depending on flour type, miller, altitude, water temp. etc., the amount of flour in a given recipe is always a guide. Again, you have to know your ingredients. You will never see 'one and an eight cup plus 2 TBSP hard flour' in a recipe, because it is so variable for many different reasons. Flour and water are the two most flexible ingredients, and are always variable. Hopefully this helps, I am sure someone will come along with a more scientific explanation for all different ingredients, I am just offering an experience based answer to your question. Also, you are right, do not mess around with baking soda and powder. If you do, you are asking for trouble. I would suppose that the rule of thumb would be that the more exacting an ingredient is (tsp, quarter tsp), you don't want to change much.